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Minimizer schemes, or just minimizers, are a very important computational primitive in sampling and sketching biological strings. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a total order $\rho$ on strings of length $k$ (also called $k$-mers). A string is processed by a sliding window algorithm that chooses, in each window of length $w+k-1$, its minimal $k$-mer with respect to $\rho$. A key characteristic of the minimizer is the expected density of chosen $k$-mers among all $k$-mers in a random infinite $\sigma$-ary string. Random minimizers, in which the order $\rho$ is chosen uniformly at random, are often used in applications. However, little is known about their expected density $\mathcal{DR}_\sigma(k,w)$ besides the fact that it is close to $\frac{2}{w+1}$ unless $w\gg k$. We first show that $\mathcal{DR}_\sigma(k,w)$ can be computed in $O(k\sigma^{k+w})$ time. Then we attend to the case $w\le k$ and present a formula that allows one to compute $\mathcal{DR}_\sigma(k,w)$ in just $O(w^2)$ time. Further, we describe the behaviour of $\mathcal{DR}_\sigma(k,w)$ in this case, establishing the connection between $\mathcal{DR}_\sigma(k,w)$, $\mathcal{DR}_\sigma(k+1,w)$, and $\mathcal{DR}_\sigma(k,w+1)$. In particular, we show that $\mathcal{DR}_\sigma(k,w)<\frac{2}{w+1}$ (by a tiny margin) unless $w$ is small. We conclude with some partial results and conjectures for the case $w>k$.

In this paper, we present and study the \emph{Hamming distance oracle problem}. In this problem, the task is to preprocess two strings $S$ and $T$ of lengths $n$ and $m$, respectively, to obtain a data-structure that is able to answer queries regarding the Hamming distance between a substring of $S$ and a substring of $T$. For a constant size alphabet strings, we show that for every $x\le nm$ there is a data structure with $\tilde{O}(nm/x)$ preprocess time and $O(x)$ query time. We also provide a combinatorial conditional lower bound, showing that for every $\varepsilon > 0$ and $x \le nm$ there is no data structure with query time $O(x)$ and preprocess time $O((\frac{nm}{x})^{1-\varepsilon})$ unless combinatorial fast matrix multiplication is possible. For strings over general alphabet, we present a data structure with $\tilde{O}(nm/\sqrt{x})$ preprocess time and $O(x)$ query time for every $x \le nm$.

A $\lambda$-cover of a string $S$ is a set of strings $\{C_i\}_1^\lambda$ such that every index in $S$ is contained in an occurrence of at least one string $C_i$. The existence of a $1$-cover defines a well-known class of quasi-periodic strings. Quasi-periodicity can be decided in linear time, and all $1$-covers of a string can be reported in linear time plus the size of the output. Since in general it is NP-complete to decide whether a string has a $\lambda$-cover, the natural next step is the development of efficient algorithms for $2$-covers. Radoszewski and Straszy\'nski [ESA 2020] analysed the particular case where the strings in a $2$-cover must be of the same length. They provided an algorithm that reports all such $2$-covers of $S$ in time near-linear in $|S|$ and in the size of the output. In this work, we consider $2$-covers in full generality. Since every length-$n$ string has $\Omega(n^2)$ trivial $2$-covers (every prefix and suffix of total length at least $n$ constitute such a $2$-cover), we state the reporting problem as follows: given a string $S$ and a number $m$, report all $2$-covers $\{C_1,C_2\}$ of $S$ with length $|C_1|+|C_2|$ upper bounded by $m$. We present an $\tilde{O}(n + Output)$ time algorithm solving this problem, with Output being the size of the output. This algorithm admits a simpler modification that finds a $2$-cover of minimum length. We also provide an $\tilde{O}(n)$ time construction of a $2$-cover oracle which, given two substrings $C_1,C_2$ of $S$, reports in poly-logarithmic time whether $\{C_1,C_2\}$ is a $2$-cover of $S$., Comment: 31 pages

Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into $S\cdot S'$ where $S'$ is the reverse complement of a prefix of $S$. Similarly, a left hairpin completion operation transforms a string $S$ into $S'\cdot S$ where $S'$ is the reverse complement of a suffix of $S$. The hairpin completion distance from $S$ to $T$ is the minimum number of hairpin completion operations needed to transform $S$ into $T$. Recently Boneh et al. showed an $O(n^2)$ time algorithm for finding the hairpin completion distance between two strings of length at most $n$. In this paper we show that for any $\varepsilon>0$ there is no $O(n^{2-\varepsilon})$-time algorithm for the hairpin completion distance problem unless the Strong Exponential Time Hypothesis (SETH) is false. Thus, under SETH, the time complexity of the hairpin completion distance problem is quadratic, up to sub-polynomial factors., Comment: To be published in CPM 2024

We introduce the natural notion of a matching frame in a $2$-dimensional string. A matching frame in a $2$-dimensional $n\times m$ string $M$, is a rectangle such that the strings written on the horizontal sides of the rectangle are identical, and so are the strings written on the vertical sides of the rectangle. Formally, a matching frame in $M$ is a tuple $(u,d,\ell,r)$ such that $M[u][\ell ..r] = M[d][\ell ..r]$ and $M[u..d][\ell] = M[u..d][r]$. In this paper, we present an algorithm for finding the maximum perimeter matching frame in a matrix $M$ in $\tilde{O}(n^{2.5})$ time (assuming $n \ge m)$. Additionally, for every constant $\epsilon> 0$ we present a near-linear $(1-\epsilon)$-approximation algorithm for the maximum perimeter of a matching frame. In the development of the aforementioned algorithms, we introduce inventive technical elements and uncover distinctive structural properties that we believe will captivate the curiosity of the community.

We give an $\tilde O(n^2)$ time algorithm for computing the exact Dynamic Time Warping distance between two strings whose run-length encoding is of size at most $n$. This matches (up to log factors) the known (conditional) lower bound, and should be compared with the previous fastest $O(n^3)$ time exact algorithm and the $\tilde O(n^2)$ time approximation algorithm.

A Dyck sequence is a sequence of opening and closing parentheses (of various types) that is balanced. The Dyck edit distance of a given sequence of parentheses $S$ is the smallest number of edit operations (insertions, deletions, and substitutions) needed to transform $S$ into a Dyck sequence. We consider the threshold Dyck edit distance problem, where the input is a sequence of parentheses $S$ and a positive integer $k$, and the goal is to compute the Dyck edit distance of $S$ only if the distance is at most $k$, and otherwise report that the distance is larger than $k$. Backurs and Onak [PODS'16] showed that the threshold Dyck edit distance problem can be solved in $O(n+k^{16})$ time. In this work, we design new algorithms for the threshold Dyck edit distance problem which costs $O(n+k^{4.544184})$ time with high probability or $O(n+k^{4.853059})$ deterministically. Our algorithms combine several new structural properties of the Dyck edit distance problem, a refined algorithm for fast $(\min,+)$ matrix product, and a careful modification of ideas used in Valiant's parsing algorithm., Comment: Journal version

The shift distance $\mathsf{sh}(S_1,S_2)$ between two strings $S_1$ and $S_2$ of the same length is defined as the minimum Hamming distance between $S_1$ and any rotation (cyclic shift) of $S_2$. We study the problem of sketching the shift distance, which is the following communication complexity problem: Strings $S_1$ and $S_2$ of length $n$ are given to two identical players (encoders), who independently compute sketches (summaries) $\mathtt{sk}(S_1)$ and $\mathtt{sk}(S_2)$, respectively, so that upon receiving the two sketches, a third player (decoder) is able to compute (or approximate) $\mathsf{sh}(S_1,S_2)$ with high probability. This paper primarily focuses on the more general $k$-mismatch version of the problem, where the decoder is allowed to declare a failure if $\mathsf{sh}(S_1,S_2)>k$, where $k$ is a parameter known to all parties. Andoni et al. (STOC'13) introduced exact circular $k$-mismatch sketches of size $\widetilde{O}(k+D(n))$, where $D(n)$ is the number of divisors of $n$. Andoni et al. also showed that their sketch size is optimal in the class of linear homomorphic sketches. We circumvent this lower bound by designing a (non-linear) exact circular $k$-mismatch sketch of size $\widetilde{O}(k)$; this size matches communication-complexity lower bounds. We also design $(1\pm \varepsilon)$-approximate circular $k$-mismatch sketch of size $\widetilde{O}(\min(\varepsilon^{-2}\sqrt{k}, \varepsilon^{-1.5}\sqrt{n}))$, which improves upon an $\widetilde{O}(\varepsilon^{-2}\sqrt{n})$-size sketch of Crouch and McGregor (APPROX'11).

We revisit the $k$-mismatch problem in the streaming model on a pattern of length $m$ and a streaming text of length $n$, both over a size-$\sigma$ alphabet. The current state-of-the-art algorithm for the streaming $k$-mismatch problem, by Clifford et al. [SODA 2019], uses $\tilde O(k)$ space and $\tilde O\big(\sqrt k\big)$ worst-case time per character. The space complexity is known to be (unconditionally) optimal, and the worst-case time per character matches a conditional lower bound. However, there is a gap between the total time cost of the algorithm, which is $\tilde O(n\sqrt k)$, and the fastest known offline algorithm, which costs $\tilde O\big(n + \min\big(\frac{nk}{\sqrt m},\sigma n\big)\big)$ time. Moreover, it is not known whether improvements over the $\tilde O(n\sqrt k)$ total time are possible when using more than $O(k)$ space. We address these gaps by designing a randomized streaming algorithm for the $k$-mismatch problem that, given an integer parameter $k\le s \le m$, uses $\tilde O(s)$ space and costs $\tilde O\big(n+\min\big(\frac {nk^2}m,\frac{nk}{\sqrt s},\frac{\sigma nm}s\big)\big)$ total time. For $s=m$, the total runtime becomes $\tilde O\big(n + \min\big(\frac{nk}{\sqrt m},\sigma n\big)\big)$, which matches the time cost of the fastest offline algorithm. Moreover, the worst-case time cost per character is still $\tilde O\big(\sqrt k\big)$., Comment: Extended abstract to appear in CPM 2020

We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution dating back to the discovery of suffix trees (Weiner, 1973) and their efficient construction for integer alphabets (Farach-Colton, 1997). However, these solutions require $\Theta(n)$ space, which is prohibitive in many applications. To address this issue, Starikovskaya and Vildh{\o}j (CPM 2013) showed that for $n^{2/3} \le s \le n^{1-o(1)}$, the LCS problem can be solved in $O(s)$ space and $O(\frac{n^2}{s})$ time. Kociumaka et al. (ESA 2014) generalized this tradeoff to $1 \leq s \leq n$, thus providing a smooth time-space tradeoff from constant to linear space. In this paper, we obtain a significant speed-up for instances where the length $L$ of the sought LCS is large. For $1 \leq s \leq n$, we show that the LCS problem can be solved in $O(s)$ space and $\tilde{O}(\frac{n^2}{L\cdot s}+n)$ time. The result is based on techniques originating from the LCS with Mismatches problem (Flouri et al., 2015; Charalampopoulos et al., CPM 2018), on space-efficient locally consistent parsing (Birenzwige et al., SODA 2020), and on the structure of maximal repetitions (runs) in the input documents.

We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several $(1+\epsilon)$-approximation algorithms have been proposed in the literature, with running time of the form $O(\epsilon^{-O(1)}n\log n\log m)$, all using fast Fourier transform (FFT). We describe a simple $(1+\epsilon)$-approximation algorithm that is faster and does not need FFT. Combining our approach with additional ideas leads to numerous new results: - We obtain the first linear-time approximation algorithm; the running time is $O(\epsilon^{-2}n)$. - We obtain a faster exact algorithm computing all Hamming distances up to a given threshold k; its running time improves previous results by logarithmic factors and is linear if $k\le\sqrt m$. - We obtain approximation algorithms with better $\epsilon$-dependence using rectangular matrix multiplication. The time-bound is $\~O(n)$ when the pattern is sufficiently long: $m\ge \epsilon^{-28}$. Previous algorithms require $\~O(\epsilon^{-1}n)$ time. - When k is not too small, we obtain a truly sublinear-time algorithm to find all locations with Hamming distance approximately (up to a constant factor) less than k, in $O((n/k^{\Omega(1)}+occ)n^{o(1)})$ time, where occ is the output size. The algorithm leads to a property tester, returning true if an exact match exists and false if the Hamming distance is more than $\delta m$ at every location, running in $\~O(\delta^{-1/3}n^{2/3}+\delta^{-1}n/m)$ time. - We obtain a streaming algorithm to report all locations with Hamming distance approximately less than k, using $\~O(\epsilon^{-2}\sqrt k)$ space. Previously, streaming algorithms were known for the exact problem with \~O(k) space or for the approximate problem with $\~O(\epsilon^{-O(1)}\sqrt m)$ space.

We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the Longest Common Extension (LCE) problem, where for some parameter $1\le\tau\le n$, the goal is to construct a data structure that uses $O(\frac {n}{\tau})$ words of space and can compute the longest common prefix length of any pair of suffixes. We show how to use ideas based on the Locally Consistent Parsing technique, that was introduced by Sahinalp and Vishkin [STOC '94], in some non-trivial ways in order to improve the known results for the above problems. We introduce new Las-Vegas and deterministic algorithms for both problems. We introduce the first Las-Vegas SST construction algorithm that takes $O(n)$ time. This is an improvement over the last result of Gawrychowski and Kociumaka [SODA '17] who obtained $O(n)$ time for Monte-Carlo algorithm, and $O(n\sqrt{\log |B|})$ time for Las-Vegas algorithm. In addition, we introduce a randomized Las-Vegas construction for an LCE data structure that can be constructed in linear time and answers queries in $O(\tau)$ time. For the deterministic algorithms, we introduce an SST construction algorithm that takes $O(n\log \frac{n}{|B|})$ time (for $|B|=\Omega(\log n)$). This is the first almost linear time, $O(n\cdot poly\log{n})$, deterministic SST construction algorithm, where all previous algorithms take at least $\Omega\left(\min\{n|B|,\frac{n^2}{|B|}\}\right)$ time. For the LCE problem, we introduce a data structure that answers LCE queries in $O(\tau\sqrt{\log^*n})$ time, with $O(n\log\tau)$ construction time (for $\tau=O(\frac{n}{\log n})$). This data structure improves both query time and construction time upon the results of Tanimura et al. [CPM '16]., Comment: Extended abstract to appear is SODA 2020

In the pattern matching with $d$ wildcards problem one is given a text $T$ of length $n$ and a pattern $P$ of length $m$ that contains $d$ wildcard characters, each denoted by a special symbol $'?'$. A wildcard character matches any other character. The goal is to establish for each $m$-length substring of $T$ whether it matches $P$. In the streaming model variant of the pattern matching with $d$ wildcards problem the text $T$ arrives one character at a time and the goal is to report, before the next character arrives, if the last $m$ characters match $P$ while using only $o(m)$ words of space. In this paper we introduce two new algorithms for the $d$ wildcard pattern matching problem in the streaming model. The first is a randomized Monte Carlo algorithm that is parameterized by a constant $0\leq \delta \leq 1$. This algorithm uses $\tilde{O}(d^{1-\delta})$ amortized time per character and $\tilde{O}(d^{1+\delta})$ words of space. The second algorithm, which is used as a black box in the first algorithm, is a randomized Monte Carlo algorithm which uses $O(d+\log m)$ worst-case time per character and $O(d\log m)$ words of space., Comment: Extended abstract appeared in ESA 2016